Habitat transformation reshapes protistan community composition and assembly processes in coastal wetlands of southeastern China

Coastal wetlands along southeastern China have undergone extensive habitat transformations, notably from natural mudflats (MFs) to Spartina alterniflora marshes (SAs) and aquaculture ponds (APs), yet the ecological consequences for sediment protistan communities remain largely unknown. Here, we systematically examined protistan diversity, community composition, functional groups, and assembly processes across 21 wetlands spanning five provinces using amplicon sequencing. Although alpha diversity remained stable across habitat types, community composition and functional group distributions were significantly altered. In particular, phototrophic protists declined markedly following S. alterniflora invasion and then increased after aquaculture pond reclamation. Meanwhile, consumer and phototroph assemblages were strongly influenced by sediment grain size. Salinity emerged as the key environmental driver of protistan diversity and community structure. Distance-decay relationships indicated elevated spatial turnover in SAs, suggesting increased environmental filtering after plant invasion. Assembly process analysis revealed a dominance of deterministic mechanisms in shaping community structure across all habitats, with the strongest signal observed in SAs. These findings demonstrate that land-use change reshapes protistan communities through altered environmental constraints, highlighting the ecological sensitivity of microbial eukaryotes to anthropogenic disturbance in coastal wetland ecosystems. IMPORTANCE Protists play essential roles in nutrient cycling, energy transfer, and microbial food web dynamics, yet their responses to anthropogenic habitat transformation in coastal wetlands remain underexplored. This study offers the first large-scale biogeographic assessment of sediment protistan communities across three contrasting coastal habitat types in southeastern China. We show that while alpha diversity remains resilient, profound shifts in community composition, functional group structure, and spatial turnover occur following Spartina alterniflora invasion and aquaculture conversion. Our findings underscore the primacy of environmental filtering, driven by salinity and sediment texture, in mediating these patterns and shaping community assembly. These insights not only expand our understanding of protistan ecology under coastal land-use change but also highlight their potential as sensitive bioindicators for monitoring ecological integrity and resilience in dynamic coastal systems.